Table 2.
Number of SNPs on each simulated panel before and after quality control for imputation to 50K or 777K SNP panels 1
| Commercial name | Label | Number of SNPs | Number of SNPs in the imputation to 50K | Number of SNPs in the imputation to 777K |
|---|---|---|---|---|
| Illumina Bovine3K | 3K | 2,900 | 2,321 | 2,359 |
| Illumina BovineLD | 6K | 6,909 | 6,205 | 6,216 |
| Beef LD GeneSeek Genomic Profiler | 8K | 8,762 | 7,033 | 7,478 |
| 15K panel2 | 15K | 14,195 | 12,304 | 12,345 |
| Indicus LD GeneSeek Genomic Profiler | 20K | 19,721 | 7,320 | 16,047 |
| Illumina BovineSNP50 | 50K | 54,609 | 43,247 | 43,247 |
| GeneSeek Genomic Profiler Indicus HD | 90iK | 74,085 | - | 55,819 |
| GeneSeek Genomic Profiler Beef HD | 90tK | 76,992 | - | 61,445 |
| Illumina BovineHD | 777K | 787,799 | - | 587,620 |
1The SNP quality control included GenCall score (> = 0.15), Call Rate (> = 0.90), Hardy-Weinberg Equilibrium (P > =10−6), removal of non-autosomal chromosomes and SNPs not in common with reference panel;
2Non commercial panel. The 15K panel was created based on the Beef LD GeneSeek Genomic Profiler (8K) panel by expanding it with SNPs selected based on minor allele frequency greater than 0.23, linkage disequilibrium less than 0.088 and preferably located evenly spaced between two SNPs in the 8K SNP panel.